"Why build an undergraduate architecture course around FPGA-based
processors and systems? Because there is such value in the experience
of building real hardware. Besides the emotional appeal of booting
a computer made of your own ideas and your own hands (and how many
educators have had that pleasure?), FPGA CPUs can impart a realism to
the learning experience that is probably not available in more textbook
or simulator-based approaches."

"So much of computer architecture is about making tradeoffs such as
performance versus area versus cycle time versus power, etc. While
there is much value in a course project to develop a processor model
in an HDL, and then study its behavior in a simulator, it doesn't go
far enough. It's like teaching how to balance a home budget but with a
bottomless checking account. By not closing the loop with some kind of
realistic cycle time, area, and resource-usage data, the design tradeoffs
aspect suffers."

Check it out - in particular, the last two pages on "advanced
computer architecture research" list some FPGA computing research topics.

[updated 02/18/01]
For an interesting student perspective on this kind of project,
please read
How the Puerco was born.